Dr. McDonald's research focuses on clinical informatics; analyzing clinical data and providing feedback to clinicians; development and study of electronic medical record systems (EMRs) and personal health records (PHRs); automatic reminder systems; promoting the development, enhancement, and adoption of clinical messaging and vocabulary standards; and using huge clinical databases and de-identifying them for clinical research use.

He has led the development of the medical informatics standards necessary for transmitting patient data from source systems to electronic medical records and research databases. He was one of the founders of the Health Level 7 (HL7) message standards, used in all hospitals today, and he also developed the Logical Observation Identifier Names and Codes (LOINC) database of universal codes for clinical observations, including laboratory tests, clinical measurements and physician reports.

In 1972, Dr. McDonald developed one of the nation's first electronic medical record systems (EMRs), the Regenstrief Medical Record System (RMRS), and directed its use in clinical trials that have illuminated the ways in which electronic records can improve patient care. He published the first randomized trials showing the benefits of computer reminder systems and of physician order entry systems. He has written more than 275 peer-reviewed articles. Additionally, he implemented the Indiana Network for Patient Care, the first community-wide health information exchange, which now carries over 4 billion clinical observations from more than 70 hospitals, and is considered a national model for regional health information exchange.

His work at NIH continues this trend. Dr. McDonald collaborates in numerous efforts to facilitate industry adoption of standard vocabularies in electronic medical records and public health reporting, as required by meaningful use regulations. He has been working with numerous NIH Institutes to align research terminology with federally mandated clinical terminologies. He emphasizes the need for using the same standards where information content overlaps between clinical and research domains (e.g. laboratory testing, vital signs, and clinical survey instruments) that can be integrated with existing clinical LOINC variables to allow data sharing and interoperability.

Dr. McDonald served as the Scientific Director of the Lister Hill National Center for Biomedical Communications at NLM from 2006-2018, overseeing all LHNCBC research and development in biomedical informatics related to consumer health, clinical data, image processing and visualization, and natural language processing. Current research projects include biomedical data visualization, high resolution electron microscopy, imaging tools for cancer research, and 3D biomedical imaging research, openI (medical citations enriched by relevant images with capacity to search by image), and automated medical text indexing research. Dr. McDonald currently serves as the NLM Chief Health Data Standards Officer.

Dr. McDonald obtained his medical degree from the University of Illinois, and completed his internship in Internal Medicine at Boston City Hospital, Harvard Medical Service, and his residency in Internal Medicine at Cook County Hospital and University of Wisconsin. Before beginning his residency, he earned an MS in Biomedical Engineering from Northwestern University, and completed a fellowship at NIH, where he managed the development of the first clinical laboratory computer system at the Clinical Research Center.

Prior to joining NLM, Dr. McDonald was Regenstrief Professor of Medical Informatics and Distinguished Professor of Medicine at the Indiana University (IU) School of Medicine and Director of the Regenstrief Institute for Health Care.

He is a member of the U.S. Department of Health and Human Services (HHS) Office of the National Coordinator (ONC) for Health Information Technology (HIT) Standards Committee's Vocabulary Task Force and Clinical Operations Workgroup. He currently chairs the LOINC Committee.